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CHARMM: The biomolecular simulation program
An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases
- F. Rosenthal, Karla L. H. Feijs, M. Hottiger
- Biology, ChemistryNature Structural &Molecular Biology
- 1 April 2013
MacroD2 reversed the ARTD10-catalyzed, mono-ADP-ribosylhydrolase–mediated inhibition of glycogen synthase kinase 3β (GSK3β) in vitro and in cells, thus underlining the physiological and regulatory importance of mono- ADP- ribosylHydrolase activity.
The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour.
- C. Kaiser-Bunbury, S. Muff, J. Memmott, C. Müller, A. Caflisch
- Environmental ScienceEcology letters
- 1 April 2010
Tolerance of generalized networks to species extinctions was high in the random removal scenario, with an increase in network stability if species formed new interactions, however, Anthropogenic disturbance that promote the extinction of the strongest interactors might induce a sudden collapse of pollination networks.
FACTS: Fast analytical continuum treatment of solvation
An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and…
PARP1 ADP-ribosylates lysine residues of the core histone tails
Computational and experimental results provide strong evidence that PARP1 modifies important regulatory lysines of the core histone tails of all core histones.
Predicting free energy changes using structural ensembles.
- A. Benedix, Caroline M Becker, B. L. de Groot, A. Caflisch, R. Böckmann
- Political ScienceNature methods
The next issue of NPG Nature Asia-Pacific will be published in May 2017, with a focus on China, Korea and South Korea.
The protein folding network.
Evaluation of a fast implicit solvent model for molecular dynamics simulations
The present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail.
Prediction of aggregation rate and aggregation‐prone segments in polypeptide sequences
- G. Tartaglia, A. Cavalli, R. Pellarin, A. Caflisch
- BiologyProtein science : a publication of the Protein…
- 1 October 2005
A model based on physicochemical properties and computational design of β‐aggregating peptide sequences is shown to be able to predict the aggregation rate over a large set of natural polypeptide sequences.
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia
The results provide the first direct evidence for epigenetic regulation of gene expression in this simple eukaryote, suggesting that regulation of histone acetylation is involved in the control ofGiardia stage differentiation, and identifies epigenetic mechanisms as a promising target to prevent Giardia transmission.